DNA‐analysis to monitor fisheries and aquaculture: Too costly?

Evidence from DNA‐analysis is commonplace in human criminal investigations, and while it is increasingly being used in wildlife crime, to date, its application to control and enforcement activities in fisheries and aquaculture has only been sporadic. Contemporary DNA‐analysis tools are capable of addressing a broad range of compliance issues, species identification, mislabelling of fish products, determining the origin of catches and the farm of origin of aquaculture escapees. Such applications have the potential to ensure traceability along the fish product supply chain and to combat consumer fraud and Illegal, Unreported and Unregulated fishing. Nevertheless, DNA‐analysis is not yet used routinely in investigations into compliance with fisheries and aquaculture legislation. One potential reason for this is that DNA‐analysis techniques may have been regarded as too expensive. However, costs have plummeted over the past decade prompting us to objectively assess whether the costs associated with routine use of DNA‐analysis techniques for fisheries and aquaculture control and enforcement activities do constitute an impediment. Based on a number of recent fisheries and aquaculture compliance investigations that incorporated DNA‐analysis, our results indicate that the use of genetic analysis was justified and worthwhile in all cases examined. We therefore conclude that the costs associated with DNA‐analysis do not represent a barrier to the routine adoption of DNA‐analysis techniques in fisheries and aquaculture compliance investigations. Thus, control and enforcement agencies should be encouraged to use such techniques routinely.     

A review of aquatic weed biology and management research conducted by the United States Department of Agriculture-Agricultural Research Service

Ever-increasing demand for water to irrigate crops, support aquaculture, provide domestic water needs and to protect natural aquatic and riparian habitats has necessitated research to reduce impacts from a parallel increase in invasive aquatic weeds. This paper reviews the past 4-5 years of research by USDA-ARS covering such areas as weed biology, ecology, physiology and management strategies, including herbicides, biological control and potential for use of natural products. Research approaches range from field-level studies to highly specific molecular and biochemical work, spanning several disciplines and encompassing the most problematic weeds in these systems. This research has led to new insights into plant competition, host-specificity, and the fate of aquatic herbicides, their modes of action and effects on the environment. Another hallmark of USDA-ARS research has been its many collaborations with other federal, state action and regulatory agencies and private industry to develop new solutions to aquatic weed problems that affect our public natural resources and commercial enterprises.     

Repeated sublethal freshwater exposures reduce the amoebic gill disease parasite,Neoparamoeba perurans,on Atlantic salmon

Freshwater bathing is one of the main treatment options available against amoebic gill disease (AGD) affecting multiple fish hosts in mariculture systems. Prevailing freshwater treatments are designed to be long enough to kill Neoparamoeba perurans, the ectoparasite causing AGD, which may select for freshwater tolerance. Here, we tested whether using shorter, sublethal freshwater treatment durations are a viable alternative to lethal ones for N. perurans (2–4 hr). Under in vitro conditions, gill‐isolated N. perurans attached to plastic substrate in sea water lifted off after ≥2 min in freshwater, but survival was not impacted until 60 min. In an in vivo experiment, AGD‐affected Atlantic salmon Salmo salar subjected daily to 30 min (sublethal to N. perurans) and 120 min (lethal to N. perurans) freshwater treatments for 6 days consistently reduced N. perurans cell numbers on gills (based on qPCR analysis) compared to daily 3 min freshwater or seawater treatments for 6 days. Our results suggest that targeting cell detachment rather than cell death with repeated freshwater treatments of shorter duration than typical baths could be used in AGD management. However, the consequences of modifying the intensity of freshwater treatment regimes on freshwater tolerance evolution in N. perurans populations require careful consideration.     

Changes in volatile compounds of carrots (Daucus carota L.) during refrigerated and frozen storage

Carrots (Daucus carota L.) of cv. Bolero and cv. Carlo were processed into shreds and stored for up to 4 months at -24 degrees C (frozen storage), or the roots were stored for up to 4 months at 1 degrees C (refrigerated storage) followed by processing into shreds. Volatiles from the carrot shreds were collected by dynamic headspace technique and analyzed by GC-FID, GC-MS, GC-MS/MS, and GC-O to determine the volatile composition and aroma active components of carrots stored under different temperature conditions. A total of 52 compounds were quantified, of which mono- and sesquiterpenes accounted for approximately 99% of the total volatile mass. Major volatile compounds were (-)-alpha-pinene, beta-myrcene, (-)-limonene, (+)-limonene, (+)-sabinene, gamma-terpinene, p-cymene, terpinolene, beta-caryophyllene, alpha-humulene, and (E)- and (Z)-gamma-bisabolene. A considerable increase in the concentration of mono- and sesquiterpenes was observed during refrigerated storage, whereas the concentration of terpenoids was around the same level during frozen storage. GC-O revealed that the major volatiles together with (+)-alpha-pinene, (-)-beta-pinene, (+)-beta-pinene, 6-methyl-5-hepten-2-one, (-)-beta-bisabolene, beta-ionone, and myristicin had an odor sensation, which included notes of "carrot top", "terpene-like", "green", "earthy", "fruity", "citrus-like", "spicy", "woody", and "sweet".     

Empirical predictions of plant material C and N mineralization patterns from near infrared spectroscopy, stepwise chemical digestion and C/N ratios

Prediction of carbon (C) and nitrogen (N) mineralization patterns of plant litter is desirable for both agronomic and environmental reasons. Near infrared reflectance (NIR) spectroscopy has recently been introduced in decomposition studies to characterize biochemical composition. The purpose of the current study was to use empirical techniques to predict C and N mineralization patterns of a wide range of plant materials incubated under controlled temperature and moisture conditions. We hypothesized that the richness of information in the NIR spectra would considerably improve predictions compared to traditional stepwise chemical digestion (SCD) or C/N ratios. Initially, we fitted a number of empirical functions to the observed C and N mineralization patterns. The best functions fitted with R²=0.990 and 0.949 to C and N, respectively. The fractions of C and N mineralized at different points in time were then either predicted directly with regression functions or indirectly by prediction of the parameters of the empirical functions fitted to incubation data. In both cases, partial least squares (PLS) regressions were used and predictions were validated by cross-validations. We found that the NIR spectra (best R²=0.925) were able to predict C mineralization patterns marginally better than the SCD fractions (best R²=0.911), but considerably better than the C/N ratios (best R²=0.851). In contrast, N mineralization was better predicted by SCD fractions (best R²=0.533) than the C/N ratio (best R²=0.497), which was better than NIR predictions (best R²=0.446). Although the predictions with the NIR spectra were only slightly better for C and worse for N mineralization compared to SCD fractions, NIR spectroscopy still holds advantages, as it is a much less laborious and cheaper analytical method. Furthermore, exploration of the applications of NIR spectroscopy in decomposition studies has only just begun, and offers new ways to gain insights into the decomposition process.     

Impacts from Deposition on Swedish Forest Ecosystems Identified by Integrated Monitoring

Integrated monitoring of ecosystems (IM) is an international co-operative programme (ICP) to control effects of air pollution and climate change on water, soil and biological systems. It is a part of the Convention on Long-Range Transboundary Air Pollution (CLRTAP) of the United Nations Economic Commission of Europe (UN/ECE). The ICP-IM is undertaken on sites/catchments to investigate acidification, eutrophication and heavy metals with an integrated approach. In Sweden, long-term time series from forest ecosystems, with a long and stable continuity, will reveal trends and changes in processes and enable modelling to be undertaken. Investigations of acidity/alkalinity in relation to mineral and organic acids indicated the importance of atmospheric deposition. Recent results show very high inorganic nitrogen retention (99%), a net loss of sulphur originating mainly from organic horizons, and a high inorganic aluminium content in the illuvial soil horizons which could be detrimental to forests. Forest deficiency could also be caused by an observed ongoing translocation of Zn to deeper soil layers implying a movement towards increased release to surface waters.     

The structure of ferrihydrite, a nanocrystalline material

Despite the ubiquity of ferrihydrite in natural sediments and its importance as an industrial sorbent, the nanocrystallinity of this iron oxyhydroxide has hampered accurate structure determination by traditional methods that rely on long-range order. We uncovered the atomic arrangement by real-space modeling of the pair distribution function (PDF) derived from direct Fourier transformation of the total x-ray scattering. The PDF for ferrihydrite synthesized with the use of different routes is consistent with a single phase (hexagonal space group P6(3)mc; a = approximately 5.95 angstroms, c = approximately 9.06 angstroms). In its ideal form, this structure contains 20% tetrahedrally and 80% octahedrally coordinated iron and has a basic structural motif closely related to the Baker-Figgis delta-Keggin cluster. Real-space fitting indicates structural relaxation with decreasing particle size and also suggests that second-order effects such as internal strain, stacking faults, and particle shape contribute to the PDFs.     

Structure of the polycrystalline zeolite catalyst IM-5 solved by enhanced charge flipping

Despite substantial advances in crystal structure determination methodology for polycrystalline materials, some problems have remained intractable. A case in point is the zeolite catalyst IM-5, whose structure has eluded determination for almost 10 years. Here we present a charge-flipping structure-solution algorithm, extended to facilitate the combined use of powder diffraction and electron microscopy data. With this algorithm, we have elucidated the complex structure of IM-5, with 24 topologically distinct silicon atoms and an unusual two-dimensional medium-pore channel system. This powerful approach to structure solution can be applied without modification to any type of polycrystalline material (e.g., catalysts, ceramics, pharmaceuticals, complex metal alloys) and is therefore pertinent to a diverse range of scientific disciplines.